The New England Aquarium is currently missing some of its star attractions — the sharks and rays that populate its Giant Ocean Tank — as a result of a flare-up of a parasite called Cryptocaryon irritans.

Though sharks and rays are not directly affected by the parasite, which only targets bonefish, they are very susceptible to the treatment, which involves adding copper to the water column. Because copper is a metal, it interferes with the unique sense of electro-reception in the sharks and makes them very uncomfortable, said aquarium spokesman Tony LaCasse.

So the sharks — three blacknoses and two bonnetheads, as well as eight rays — were moved to the aquarium’s offsite facility in the Fore River Shipyard in Quincy while the water in the tank is being treated.

The animals in the hugely popular shark and ray “touch tank” were unaffected, and remain on exhibit in Boston.

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The parasite embeds itself on the skin of fish, particularly around the gills and fins, and irritates the fish, causing them to rub and scratch profusely, which can lead to sores that can become infected, LaCasse said.

Often called marine ich or white spot disease, the parasite is extremely common in the aquarium world. It is always around and occasionally flares up — the New England Aquarium sees an outbreak every two to five years — but is a near constant bane for those who have home aquariums.

This recent outbreak is not unexpected because it comes just after the aquarium reopened its signature Giant Ocean Tank following a $17.3 million renovation.

“Because we shut down the Giant Ocean Tank for the renovation, we were essentially sterilizing and restarting the system,” said Mark Smith, the vice president of animal care. “So what we’re seeing are the symptoms of an environment that’s still stabilizing in the tank.”

Smith likened the ecosystem in the new tank to a weakened immune system and said the tank had essentially come down with a cold. “Now, we’re in the process of rebuilding that immune system,” he said.

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The outbreak was first noticed this winter, and a decision was made to move the sharks to the aquarium’s animal care facility in Quincy, which was constructed so they would have a place to store the animals from the Giant Ocean Tank during the renovation.

Moving sharks is a delicate process, highly stressful for the animals, that involves catching them in a net, loading them into a box truck that has a water tank inside, and then hustling down the Southeast Expressway.

They had hoped to return the sharks to the tank in time for April school vacation, but another flare-up of the parasite kept them in Quincy. Things are looking better now, Smith said, and the sharks may return in the next week or two. But if the ecosystem in the tank does not stabilize, the aquarium is exploring another treatment to combat the parasites that would involve cutting the salinity in the tank water in half. To do that, they would need to bring in 15 tanker trucks full of clean freshwater.

Matthew J. Lee/Globe Staff

A blacknose shark is one of five sharks moved to Quincy while the aquarium treats its Giant Ocean Tank for a parasite.

The questions about missing sharks began before the parasite broke out. When the renovated tank opened last June, the sand tiger sharks, 8-foot behemoths that swam slowly past the windows for generations of visitors, were not included in the new exhibit. That is because the new Giant Ocean Tank is designed to replicate a Caribbean reef, and that species would not typically be found there. Instead, the new exhibit features the bonnetheads, a small type of hammerhead shark, and the 4-foot blacknose sharks, which are common in the Caribbean and behave “more sharklike,” darting around in a predatory fashion, LaCasse said.

On Friday, as the school vacation crowd jammed the aquarium — the line to get in was so long that they had a juggler entertaining people while they waited — few seemed to notice that the tank was missing some of its stars.

“I want to see if there are any hammerheads,” Emma Bell, 7, of Plymouth, said as she spotted a plaque describing the bonnetheads. She stuck her face to the glass, looked inside the tank, and was quickly distracted.

“A scuba diver! And a turtle!” she yelled as she continued up the ramp, chasing after them.